2.  The replication of DNA takes place in S phase of interphase  However, DNA is also used during G 1 to assemble proteins  This process is broken down into two distinct segments: transcription and translation  The entire human genome is found in every cell, but only a portion is activated  This portion has to convey the message outside the nucleus

3.  It is not possible to translate a gene directly to a protein  RNA has to be used as an intermediary  Quite similar to DNA, with a few key differences  Structurally, it contains a ribose sugar ◦ This has a hydroxyl group in the 2’ position instead of a hydrogen

5.  Additionally, RNA tends to be single stranded, and contains uracil in the place of thymine

6.  DNA is not capable of leaving the nucleus  A complement of one of the strands is transcribed as RNA ◦ Called messenger RNA (mRNA)  RNA polymerase (II in eukaryotes) serves the duel purpose of splitting the strand and attaching the complementary nucleotides ◦ Again, in the 5’->3’ direction  This binding is not random  A region of DNA, called the promoter, initiates transcription  The order of nucleotides in the promoter determines which strand gets transcribed

7.  A series of proteins, called transcription factors, bind to the promoter ◦ For example, a TATA box is a part of the promoter region  The group of TFs and RNA pol is called a transcription initiation complex

9.  Transcription proceeds until a terminator is reached  The actual detachment process is still a bit “iffy”

10.  The form of mRNA detaching from the DNA is not ready to be read yet  It must go through two processes 1.Alteration of endings 2.Splicing of regions

11.  The 5’ end gets “capped” by a modified version of guanine  This 5’ cap holds the pre-mRNA together and acts as a recognition molecule for ribosomes  On the 3’ end, a region of 30 to 200 adenine nucleotides is added – called a poly(A) tail ◦ Again, to assist in holding the pre-mRNA together

13.  A large portion of the pre-mRNA will not leave the nucleus  Portions are cut out, and the flanking regions are joined together  The regions that are kept are exons, ones that are not are introns

15.  Short regions of nucleotides at the end of introns signal their removal  Small nuclear ribonucleoproteins, snRNPs, join up with other proteins to form a spliceosome ◦ This carries out the splicing process ◦ http://www.youtube.com/watch?v=WsofH466lqk&f eature=related http://www.youtube.com/watch?v=WsofH466lqk&f eature=related

16.  Now the mRNA is ready to be translated  Recall that the message is “read” three nucleotides at a time  This is the codon triplet

17.  The codon is interpreted by transfer RNA (tRNA)  Each version has a nucleotide triplet of its own  This serves as the complement to the codon of mRNA ◦ Hence, it is the anticodon  All 64 permutations are covered by tRNA molecules, carrying the 20 different amino acids ◦ However, there are only about 45 difference tRNA molecules

18.  In many cases, the first two nucleotides are sufficient for recognition

19.  However, each tRNA carries one, and only one, amino acid  The attachment of tRNA to amino acid is mediated by an aminoacyl-tRNA synthetase enzyme ◦ 20 different versions, one for each amino acid

21.  The interaction of tRNA and mRNA takes place in a ribosome  Consists of two protein subunits and ribosomal RNA (rRNA)  Within the ribosome are three binding sites ◦ P site (peptidyl-tRNA site) where the tRNA holding the polypepetide chain ◦ A site (aminoacyl-tRNA site) where next tRNA in line is held ◦ E site (exit site) where used tRNAs are discharged

23.  Begins with initiation  Small subunit of ribosome attaches to leader segment of mRNA  Initiator tRNA bearing methionine then attaches, followed by attachment of large ribosomal subunit  Although methionine is initially attached, it is sometimes removed  The next stage, elongation, is now set

24.  This is broken into three distinct steps 1.Codon recognition – mRNA codon hydrogen bonds with tRNA anticodon in A site 2.Peptide bond formation – rRNA molecule catalyzes formation of peptide bond (amino acid-amino acid bond) between adjacent amino acids in A and P sites 3.Translocation – amino acid in A site is moved to P site, and is now carrier of growing polypeptide chain (AA in P site moved to E site for removal)

25. http://www.youtube.com/watch?v=5bLEDd- PSTQ&feature=related

26.  Translation is finalized during termination  Three stop codon triplets UAA, UAG and UGA, do not code for any amino acid  Rather, a protein called a release factor binds to stop codon, causes a water molecule to attach  The polypeptide chain is released and is ready for the folding process that will make it a functional protein

27. http://www.youtube.com/watch?v=SMtWvDbfHLo&feature=relmfu http://www.youtube.com/watch?v=TfYf_rPWUdY&feature=relmfu